I assumed the answer is yes. As it doesn't say anything about what type of ship.

But if the Transport runs into one of your own ships. Your ship is also destroyed correct?

Yes. X-Wings go squish easier than Lambdas (Lambdi? Lambdites?) after all. But since you are the one setting the dials, try not to do this.

Yep. Ran over my own a-wing just last night (Tycho, still with an assault missile and completely undamaged). Wow would that assault missile have been useful.

I just got done playing my first game with the Transport and it was a slaughter. I ended up taking out 4 of their ships with it but it got extremely tough at times trying to not run over mine. I figured that was the correct way to do it but wanted to double check.